> Well, let's take the chimp/human split as an example. Do we have a
> process? Yes. First, we have sex. We have empirical evidence that organisms
> do not reproduce exactly. We have evidence that relatively few changes in
> the development pathways of organisms may have large effects of morphology
> -- Changes that even retain or enhance viability. We have evidence that
> chimp and human genomes exhibit _tiny_ differences, no greater than what
> has even been seen among organisms of the same species. We have observed
> numerous modes of speciation in the wild and a few in the lab. We have
> observed and even understand the biochemical basis of the generation of
> genomic variation. Basically, we have ample evidence that populations
> diverge genetically over time and frequently speciate. We may not
> know what drives or supports divergence, but it is an observed reality.
> Determining whether a process occurred is simple, knowing the exact
> the mechanism/s involved at any particular time is the problem.
>

One thing that does puzzle me is how the chromosomes of
related species can be so different in there arrangement
in the respective genomes. For example, morphologically,
the mouse and the rat look quite similar. Yet the
arrangement of the genes on the respective organisms seems
very different. Likewise, often the introns also seem to
have almost no homology.

I don't say this to argue, but unlike Li's lucid
description of the globin gene, I find the speciation
process quite baffling. In my ignorance at least, I
would have expected it to be rather similar.